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Background  Genital chlamydia infection is the most commonly diagnosed sexually transmitted infection in the UK.  C. trachomatis  genital infections are usually caused by strains which fall into two pathovars: lymphogranuloma venereum (LGV) and the genitourinary genotypes D–K. Although these genotypes can be discriminated by outer membrane protein gene ( omp A) sequencing or multi-locus sequence typing (MLST), neither protocol affords the high-resolution genotyping required for local epidemiology and accurate contact-tracing.    Principal Findings  We evaluated variable number tandem repeat (VNTR) and  omp A sequencing (now called multi-locus VNTR analysis and  omp A or “MLVA- omp A”) to study local epidemiology in Southampton over a period of six months. One hundred and fifty seven endocervical swabs that tested positive for  C. trachomatis  from both the Southampton genitourinary medicine (GUM) clinic and local GP surgeries were tested by COBAS Taqman 48 (Roche) PCR for the presence of  C. trachomatis . Samples tested as positive by the commercial NAATs test were genotyped, where possible, by a MLVA- omp A sequencing technique. Attempts were made to isolate  C. trachomatis  from all 157 samples in cell culture, and 68 (43%) were successfully recovered by repeatable passage in culture. Of the 157 samples, 93 ( i.e.  59%) were fully genotyped by MLVA- omp A. Only one mixed infection (E & D) in a single sample was confirmed. There were two distinct D genotypes for the  omp A gene. Most frequent  omp A genotypes were D, E and F, comprising 20%, 41% and 16% of the type-able samples respectively. Within all genotypes we detected numerous MLVA sub-types.    Conclusions  Amongst the common genotypes, there are a significant number of defined MLVA sub-types, which may reflect particular background demographics including age group, geography, high-risk sexual behavior, and sexual networks.

Evaluation of a High Resolution Genotyping Method for Chlamydia trachomatis Using Routine Clinical Samples